bpp-phyl3
3.0.0
Toggle main menu visibility
Main Page
Namespaces
Namespace List
Namespace Members
All
a
b
c
d
e
f
g
h
i
l
m
n
o
p
r
s
t
v
w
z
Functions
a
c
d
e
f
g
h
i
l
m
o
p
r
t
w
z
Variables
Typedefs
a
b
c
d
e
f
i
l
m
n
p
r
s
t
v
Enumerations
Classes
Class List
Class Hierarchy
Class Members
All
a
b
c
d
e
f
g
h
i
j
k
l
m
n
o
p
q
r
s
t
u
v
w
x
y
z
~
Functions
a
b
c
d
e
f
g
h
i
j
k
l
m
n
o
p
q
r
s
t
u
v
w
y
z
~
Variables
a
b
c
d
e
f
g
h
i
j
k
l
m
n
o
p
q
r
s
t
u
v
w
x
y
z
Typedefs
a
b
d
e
f
i
l
m
n
r
s
t
v
Enumerations
Enumerator
Related Functions
a
c
d
e
f
g
i
l
o
p
r
s
t
Files
File List
File Members
All
Functions
Typedefs
Macros
•
All
Classes
Namespaces
Files
Functions
Variables
Typedefs
Enumerations
Enumerator
Friends
Macros
Pages
- a -
AAExteriorSubstitutionRegister() :
bpp::AAExteriorSubstitutionRegister
aaFitness() :
bpp::AbstractCodonAAFitnessSubstitutionModel
AAInteriorSubstitutionRegister() :
bpp::AAInteriorSubstitutionRegister
aaModel() :
bpp::AbstractCodonAARateSubstitutionModel
abs() :
bpp::ExtendedFloat
AbstractAgglomerativeDistanceMethod() :
bpp::AbstractAgglomerativeDistanceMethod
AbstractAlignedPhyloLikelihood() :
bpp::AbstractAlignedPhyloLikelihood
AbstractAlignedPhyloLikelihoodSet() :
bpp::AbstractAlignedPhyloLikelihoodSet
AbstractAutonomousSubstitutionProcess() :
bpp::AbstractAutonomousSubstitutionProcess
AbstractBiblioMixedTransitionModel() :
bpp::AbstractBiblioMixedTransitionModel
AbstractBiblioSubstitutionModel() :
bpp::AbstractBiblioSubstitutionModel
AbstractBiblioTransitionModel() :
bpp::AbstractBiblioTransitionModel
AbstractCodonAAFitnessSubstitutionModel() :
bpp::AbstractCodonAAFitnessSubstitutionModel
AbstractCodonAARateSubstitutionModel() :
bpp::AbstractCodonAARateSubstitutionModel
AbstractCodonBGCSubstitutionModel() :
bpp::AbstractCodonBGCSubstitutionModel
AbstractCodonClusterAASubstitutionModel() :
bpp::AbstractCodonClusterAASubstitutionModel
AbstractCodonCpGSubstitutionModel() :
bpp::AbstractCodonCpGSubstitutionModel
AbstractCodonDistanceSubstitutionModel() :
bpp::AbstractCodonDistanceSubstitutionModel
AbstractCodonFitnessSubstitutionModel() :
bpp::AbstractCodonFitnessSubstitutionModel
AbstractCodonFrequenciesSubstitutionModel() :
bpp::AbstractCodonFrequenciesSubstitutionModel
AbstractCodonPhaseFrequenciesSubstitutionModel() :
bpp::AbstractCodonPhaseFrequenciesSubstitutionModel
AbstractCodonSubstitutionModel() :
bpp::AbstractCodonSubstitutionModel
AbstractDendrogramPlot() :
bpp::AbstractDendrogramPlot
AbstractDFPSubstitutionModel() :
bpp::AbstractDFPSubstitutionModel
AbstractDiscreteRatesAcrossSitesTreeLikelihood() :
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood
AbstractFrequencySet() :
bpp::AbstractFrequencySet
AbstractFromSubstitutionModelTransitionModel() :
bpp::AbstractFromSubstitutionModelTransitionModel
AbstractHomogeneousTreeLikelihood() :
bpp::AbstractHomogeneousTreeLikelihood
AbstractIMultiPhyloDAG() :
bpp::AbstractIMultiPhyloDAG
AbstractIMultiPhyloTree() :
bpp::AbstractIMultiPhyloTree
AbstractIMultiTree() :
bpp::AbstractIMultiTree
AbstractIPhyloDAG() :
bpp::AbstractIPhyloDAG
AbstractIPhyloTree() :
bpp::AbstractIPhyloTree
AbstractITree() :
bpp::AbstractITree
AbstractKroneckerCodonSubstitutionModel() :
bpp::AbstractKroneckerCodonSubstitutionModel
AbstractKroneckerWordSubstitutionModel() :
bpp::AbstractKroneckerWordSubstitutionModel
AbstractLkTransitionModel() :
bpp::AbstractLkTransitionModel
AbstractMapping() :
bpp::AbstractMapping
AbstractMixedTransitionModel() :
bpp::AbstractMixedTransitionModel
AbstractMutationProcess() :
bpp::AbstractMutationProcess
AbstractNonHomogeneousTreeLikelihood() :
bpp::AbstractNonHomogeneousTreeLikelihood
AbstractNucleotideSubstitutionModel() :
bpp::AbstractNucleotideSubstitutionModel
AbstractOMultiPhyloDAG() :
bpp::AbstractOMultiPhyloDAG
AbstractOMultiPhyloTree() :
bpp::AbstractOMultiPhyloTree
AbstractOMultiTree() :
bpp::AbstractOMultiTree
AbstractOPhyloDAG() :
bpp::AbstractOPhyloDAG
AbstractOPhyloTree() :
bpp::AbstractOPhyloTree
AbstractOTree() :
bpp::AbstractOTree
AbstractParametrizableSequencePhyloLikelihood() :
bpp::AbstractParametrizableSequencePhyloLikelihood
AbstractPhyloLikelihood() :
bpp::AbstractPhyloLikelihood
AbstractPhyloLikelihoodSet() :
bpp::AbstractPhyloLikelihoodSet
AbstractProteinSubstitutionModel() :
bpp::AbstractProteinSubstitutionModel
AbstractReversibleNucleotideSubstitutionModel() :
bpp::AbstractReversibleNucleotideSubstitutionModel
AbstractReversibleProteinSubstitutionModel() :
bpp::AbstractReversibleProteinSubstitutionModel
AbstractReversibleSubstitutionModel() :
bpp::AbstractReversibleSubstitutionModel
AbstractReward() :
bpp::AbstractReward
AbstractRewardMapping() :
bpp::AbstractRewardMapping
AbstractSequencePhyloLikelihood() :
bpp::AbstractSequencePhyloLikelihood
AbstractSingleDataPhyloLikelihood() :
bpp::AbstractSingleDataPhyloLikelihood
AbstractSinglePhyloSubstitutionMapping() :
bpp::AbstractSinglePhyloSubstitutionMapping
AbstractStateMap() :
bpp::AbstractStateMap
AbstractSubstitutionCount() :
bpp::AbstractSubstitutionCount
AbstractSubstitutionDistance() :
bpp::AbstractSubstitutionDistance
AbstractSubstitutionMapping() :
bpp::AbstractSubstitutionMapping
AbstractSubstitutionModel() :
bpp::AbstractSubstitutionModel
AbstractSubstitutionProcess() :
bpp::AbstractSubstitutionProcess
AbstractSubstitutionRegister() :
bpp::AbstractSubstitutionRegister
AbstractTotallyWrappedSubstitutionModel() :
bpp::AbstractTotallyWrappedSubstitutionModel
AbstractTotallyWrappedTransitionModel() :
bpp::AbstractTotallyWrappedTransitionModel
AbstractTransitionModel() :
bpp::AbstractTransitionModel
AbstractTreeDrawing() :
bpp::AbstractTreeDrawing
AbstractTreeLikelihood() :
bpp::AbstractTreeLikelihood
AbstractTreeLikelihoodData() :
bpp::AbstractTreeLikelihoodData
AbstractTreeParsimonyData() :
bpp::AbstractTreeParsimonyData
AbstractTreeParsimonyScore() :
bpp::AbstractTreeParsimonyScore
AbstractWeightedSubstitutionCount() :
bpp::AbstractWeightedSubstitutionCount
AbstractWordFrequencySet() :
bpp::AbstractWordFrequencySet
AbstractWordSubstitutionModel() :
bpp::AbstractWordSubstitutionModel
AbstractWrappedModel() :
bpp::AbstractWrappedModel
AbstractWrappedSubstitutionModel() :
bpp::AbstractWrappedSubstitutionModel
AbstractWrappedTransitionModel() :
bpp::AbstractWrappedTransitionModel
accessValueConst() :
bpp::Value< T >
accessValueMutable() :
bpp::Value< T >
accessVariableNode() :
bpp::AbstractPhyloLikelihood
addBipartition() :
bpp::BipartitionList
addDistribution() :
bpp::SubstitutionProcessCollection
addEmptyHyperNode() :
bpp::MixedSubstitutionModelSet
addEvent() :
bpp::MutationPath
addFrequencies() :
bpp::SubstitutionProcessCollection
addHyperNode() :
bpp::MixedSubstitutionModelSet
addListener() :
bpp::TreeDrawingDisplayControler
addModel() :
bpp::AbstractSinglePhyloSubstitutionMapping
,
bpp::NonHomogeneousSubstitutionProcess
,
bpp::SubstitutionModelSet
,
bpp::SubstitutionProcessCollection
,
bpp::SubstitutionProcessCollectionMember
addModelPath() :
bpp::ModelScenario
addNode() :
bpp::SiteSimulationResult
addNsParameter() :
bpp::AbstractCodonAAFitnessSubstitutionModel
addOnePerBranchSubstitutionProcess() :
bpp::SubstitutionProcessCollection
addParametrizable() :
bpp::SubstitutionProcessCollection
addPhyloLikelihood() :
bpp::AbstractAlignedPhyloLikelihoodSet
,
bpp::AbstractPhyloLikelihoodSet
,
bpp::PhyloLikelihoodContainer
,
bpp::PhyloLikelihoodSetInterface
addRateParameter() :
bpp::AbstractBiblioTransitionModel
,
bpp::AbstractFromSubstitutionModelTransitionModel
,
bpp::AbstractTransitionModel
,
bpp::BranchModelInterface
,
bpp::FromMixtureSubstitutionModel
,
bpp::G2001
,
bpp::InMixedSubstitutionModel
,
bpp::MultinomialFromTransitionModel
,
bpp::RegisterRatesSubstitutionModel
,
bpp::TransitionFromTransitionModel
,
bpp::TS98
addRegister() :
bpp::VectorOfSubstitutionRegisters
addScenario() :
bpp::SubstitutionProcessCollection
addSon() :
bpp::AwareNode
,
bpp::Node
addSubstitutionProcess() :
bpp::SubstitutionProcessCollection
addSubstitutionProcessCollectionMember() :
bpp::PhylogeneticsApplicationTools
addSubTree() :
bpp::Node
,
bpp::PhyloTree
addToHyperNode() :
bpp::MixedSubstitutionModelSet
addToModel() :
bpp::MixedSubstitutionModelSet::HyperNode
,
bpp::ModelPath
addTopologyListener() :
bpp::NNITopologySearch
,
bpp::TopologySearch
addTree() :
bpp::SubstitutionProcessCollection
addTreeDrawingListener() :
bpp::AbstractTreeDrawing
,
bpp::TreeDrawing
addTrivialBipartitions() :
bpp::BipartitionList
addX() :
bpp::Cursor
addY() :
bpp::Cursor
afterDrawBranch() :
bpp::BootstrapValuesTreeDrawingListener
,
bpp::BranchLengthsTreeDrawingListener
,
bpp::TreeDrawingListener
,
bpp::TreeDrawingListenerAdapter
afterDrawNode() :
bpp::LabelCollapsedNodesTreeDrawingListener
,
bpp::LabelInnerNodesTreeDrawingListener
,
bpp::LeafNamesTreeDrawingListener
,
bpp::NodesIdTreeDrawingListener
,
bpp::TreeDrawingListener
,
bpp::TreeDrawingListenerAdapter
afterDrawTree() :
bpp::TreeDrawingListener
,
bpp::TreeDrawingListenerAdapter
AgglomerativeDistanceMethodInterface() :
bpp::AgglomerativeDistanceMethodInterface
aliasParameters() :
bpp::SubstitutionProcessCollection
AlignedLikelihoodCalculation() :
bpp::AlignedLikelihoodCalculation
alignedLikelihoodCalculation() :
bpp::AlignedPhyloLikelihoodAutoCorrelation
,
bpp::AlignedPhyloLikelihoodHmm
,
bpp::AlignedPhyloLikelihoodInterface
,
bpp::AlignedPhyloLikelihoodMixture
,
bpp::AlignedPhyloLikelihoodProduct
,
bpp::AutoCorrelationProcessPhyloLikelihood
,
bpp::HmmProcessPhyloLikelihood
,
bpp::MixtureProcessPhyloLikelihood
,
bpp::OnABranchPhyloLikelihood
,
bpp::OneProcessSequencePhyloLikelihood
,
bpp::PartitionProcessPhyloLikelihood
,
bpp::SingleProcessPhyloLikelihood
alignedPhyloLikelihood() :
bpp::AbstractAlignedPhyloLikelihoodSet
,
bpp::AlignedPhyloLikelihoodSetInterface
,
bpp::HmmPhyloAlphabet
AlignedPhyloLikelihoodAutoCorrelation() :
bpp::AlignedPhyloLikelihoodAutoCorrelation
AlignedPhyloLikelihoodHmm() :
bpp::AlignedPhyloLikelihoodHmm
AlignedPhyloLikelihoodInterface() :
bpp::AlignedPhyloLikelihoodInterface
AlignedPhyloLikelihoodMixture() :
bpp::AlignedPhyloLikelihoodMixture
AlignedPhyloLikelihoodProduct() :
bpp::AlignedPhyloLikelihoodProduct
allelicAlphabet() :
bpp::POMO
allowWithin() :
bpp::CategorySubstitutionRegister
alphabet() :
bpp::AbstractFrequencySet
,
bpp::AbstractStateMap
,
bpp::AbstractSubstitutionRegister
,
bpp::AbstractTransitionModel
,
bpp::AbstractWrappedModel
,
bpp::BranchModelInterface
,
bpp::FrequencySetInterface
,
bpp::GivenDataSubstitutionProcessSequenceSimulator
,
bpp::MarkovModulatedSubstitutionModel
,
bpp::MutationPath
,
bpp::NonHomogeneousSequenceSimulator
,
bpp::RegisterRatesSubstitutionModel
,
bpp::SequenceSimulatorInterface
,
bpp::SimpleSubstitutionProcessSequenceSimulator
,
bpp::SimpleSubstitutionProcessSiteSimulator
,
bpp::SiteSimulationResult
,
bpp::SiteSimulatorInterface
,
bpp::StateMapInterface
,
bpp::SubstitutionModelSet
,
bpp::SubstitutionProcessSequenceSimulator
,
bpp::SubstitutionRegisterInterface
alphabetIndex() :
bpp::AbstractReward
alphabetIndexHasChanged() :
bpp::AbstractReward
,
bpp::DecompositionReward
AncestralStateReconstruction() :
bpp::AncestralStateReconstruction
AnonymousSubstitutionModel() :
bpp::AnonymousSubstitutionModel
appendModel() :
bpp::PairedSiteLikelihoods
appendModels() :
bpp::PairedSiteLikelihoods
applyParameters() :
bpp::AbstractHomogeneousTreeLikelihood
,
bpp::AbstractNonHomogeneousTreeLikelihood
areAllCompatible() :
bpp::BipartitionList
areAllCompatibleWith() :
bpp::BipartitionList
areCompatible() :
bpp::BipartitionList
,
bpp::BipartitionTools
areIdentical() :
bpp::BipartitionList
,
bpp::BipartitionTools
AutoCorrelationProcessPhyloLikelihood() :
bpp::AutoCorrelationProcessPhyloLikelihood
AutoCorrelationSequenceEvolution() :
bpp::AutoCorrelationSequenceEvolution
AwareNode() :
bpp::AwareNode
Generated on Tue Jun 10 2025 12:12:11 for bpp-phyl3 by
1.9.4